BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472532.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 19,821,760 number of mapped reads = 19,601,210 (98.89%) number of supplementary alignments = 78,295 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,828,712 number of mapped paired reads (second in pair) = 9,772,498 number of mapped paired reads (both in pair) = 19,488,998 number of mapped paired reads (singletons) = 112,212 number of mapped bases = 1,930,294,809 bp number of sequenced bases = 1,930,054,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,851,430 duplication rate = 47.12% >>>>>>> Insert size mean insert size = 30,717.8626 std insert size = 1,730,289.9404 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 54.9918 >>>>>>> ACTG content number of A's = 528,179,359 bp (27.37%) number of C's = 439,648,023 bp (22.78%) number of T's = 526,500,707 bp (27.28%) number of G's = 435,426,413 bp (22.56%) number of N's = 300,127 bp (0.02%) GC percentage = 45.34% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 11,373,695 number of insertions = 102,759 mapped reads with insertion percentage = 0.52% number of deletions = 96,921 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.6235X std coverageData = 22.2046X There is a 5.8% of reference with a coverageData >= 1X There is a 2.62% of reference with a coverageData >= 2X There is a 1.15% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 254725680 1.0219660796752839 38.96950670757582 chr2 243199373 139084278 0.5718940648749123 20.423287732215634 chr3 198022430 256332515 1.2944620212972844 29.08576637247205 chr4 191154276 57713583 0.3019214856590495 16.084543238595682 chr5 180915260 86039726 0.47558025785110664 18.469255934770455 chr6 171115067 84585048 0.4943167745713474 14.131287840425086 chr7 159138663 73684764 0.4630223894742662 18.724757807672855 chr8 146364022 74120286 0.5064105576437357 16.773450280478258 chr9 141213431 126464543 0.8955560537297618 27.76155436367552 chr10 135534747 54536168 0.40237776073762105 12.98852992255015 chr11 135006516 92783463 0.687251739760472 23.09701687366441 chr12 133851895 110017183 0.8219322034999953 26.83415846097968 chr13 115169878 45296940 0.39330544398076034 16.39261061272232 chr14 107349540 34144619 0.3180695417977571 11.07160325414525 chr15 102531392 56980378 0.5557359252471672 21.0969325721564 chr16 90354753 58305095 0.645290845961363 18.016779489472246 chr17 81195210 73246035 0.9020979809030607 20.431529077281247 chr18 78077248 60637039 0.7766287946009572 33.9940292276968 chr19 59128983 37921387 0.6413333204124279 17.145984268802476 chr20 63025520 43914182 0.6967682614915355 23.919249195738864 chr21 48129895 7540671 0.1566733316164517 6.786622059342773 chr22 51304566 15876928 0.30946422975296195 9.463290081849715 chrMT 16571 1715 0.10349405588075554 0.346321975911152 chrX 155270560 84066236 0.5414177420368678 14.499821286996996 chrY 59373566 2276347 0.03833940174656176 1.1641222721115532